The file src/configure.in needs a small patch to get Code::Blocks revision 2695 and newer compiled on Linux using the autotools:
Index: configure.in
===================================================================
--- configure.in (revision 2699)
+++ configure.in (working copy)
@@ -169,6 +169,8 @@
src/plugins/projectwizard/resources/ogre/files/Makefile
src/plugins/projectwizard/resources/smartwin/Makefile
src/plugins/projectwizard/resources/smartwin/files/Makefile
+ src/plugins/projectwizard/resources/win32gui/Makefile
+ src/plugins/projectwizard/resources/win32gui/files/Makefile
src/plugins/projectwizard/resources/wxwidgets/Makefile
src/plugins/projectwizard/resources/wxwidgets/common/Makefile
src/plugins/projectwizard/resources/wxwidgets/pch/Makefile
